Journal of Virological Methods

Data used for figures in the manuscript " Impact of nucleic acid extraction platforms on hepatitis virus genome detection".

Raw data from the validation of the Abbott RealTime CMV/EBV maxCycle protocol using WHO International Standards

These documents contain some important dates about the development and evaluation of this RT-iiPCR of DHAV-3. And we listed as follows: Fig 1 The linear relation of every dilution detected by rRT-PCR. Table 1 Reference strains and isolates used in this study for specificity testing of RT-iiPCR. Table 2 Primer information rRT-PCR assay. Table 3 Evaluation of the sensitivity of the rRT-PCR and RT-iiPCR assays to DHAV-3. Table 4 Performance evaluations of the PetNADTM and TRizol RNA extraction methods for the detection of DHAV-3 by rRT-PCR and RT-iiPCR, respectively. Table 5 The Contingency table for analysis of the level of agreement between the rRT-PCR and the RT-iiPCR assays for the detection of DHAV-3 in liver samples.

raw data for FMA reads

Table supplyments

Figure supplyment

Data from quantitative RT-PCR Data from transmission electron microscopy Data from TCID50 assays Data from iodixanol gradients

Data of RT-PCR optimization

Figure captions Fig. 1. Optimization of the LAMP assay. F1a: The effect of the MgCl2 concentrations on the LAMP reaction at 63°C. Lanes 1–8 correspond to the 2, 3, 4, 5, 6, 7, 8 and 9 mM MgSO4 concentrations. F1b: The effect of the dNTPs on the LAMP reaction using 8 mM MgSO4. Lanes 1–7 correspond to the 0.8, 1.0, 1.2, 1.4, 1.6, 1.8 and 2.0 mM dNTP concentrations. F1c: The effect of temperature on the LAMP reaction using 8 mM MgSO4 and 1.6 mM dNTPs. Lanes 1–6 corresponsd to the temperatures of 60°C, 61°C, 62°C, 63°C, 64°C and 65°C. F1d: The effect of reaction time on the LAMP assay using 8 mM MgSO4 and 1.6 mM dNTPs at 65°C. Lanes 1–6 correspond to 15, 30, 45, 60, 75 and 90 min. M: DNA marker DL2000. Fig. 2. The effect of the ratio of the FIP and BIP primers to the F3 and B3 primers on the LAMP assay using 8 mM MgSO4 and 1.6 mM dNTPs at 65°C. Lanes 1–11 correspond to 1:1-11:1. M: DNA marker DL2000. Fig. 3. Test of the specificity of LAMP. Lane M, DNA marker DL2000; lane 1, healthy tobacco leaves; lane 2, MDV-infected tobacco leaves; lane 3, TYLCV-infected tobacco leaves; lane 4, TbCSV-infected tobacco leaves; lane 5, TbLCV-infected tobacco leaves; and lane 6, positive control. Fig. 4. Comparison of the relative sensitivities of LAMP and PCR for MDV detection. F4a: lane 1, distilled water; lanes 2-8, DNA concentrations of 100, 10, 1, 0.1, 0.01, 0.001 and 0.0001 ng. F4b: lane 1, distilled water; lanes 2-8, DNA concentrations of 100, 10, 1, 0.1, 0.01, 0.001 and 0.0001 ng. Lane 9, positive control. M: DNA marker DL2000. Fig. 5. The detection of natural viral infection in selected field-grown tobacco samples using LAMP. F5a: lane 1, distilled water; lanes 2-12 tobacco samples showing MDV or virus-like symptoms; lane 13: positive control. F5b: Visual inspection of the MDV LAMP products. All products in the reaction tubes were stained with SYBR Green I. A positive reaction appeared green and a negative reaction appeared orange in daylight. F5c: A positive reaction was indicated by green fluorescence and a negative reaction was indicated by fluorescence under a UV lamp. The number of F5b and F5c is consistent with F5a. M: DNA marker DL2000.

Distribution of reads generated by the MinION runs, referred to in the Results section of manuscript as supplementary figures S1 and S2